I thought hard about it and I can finally cause the issue reproducibly. I am sometimes switching between two desks, and for some reason the monitors are attached differently on different desks, so I head into View Options and drop monitor 2 to the right or left side of monitor 1, to match the actual hardware.
Playing around with the toolbox position, I found:
If my monitors are [1] [2] the X position is between 0 and 3840
If my monitors are [2] [1] the X position is between -1920 and 1920
So that's why the toolbox didn't show, I tried to get rid of it and pulled it onto the [2] screen, which's coordinates are outside the visible area on the other dual-view setup.